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    LY75 lymphocyte antigen 75 [ Homo sapiens (human) ]

    Gene ID: 4065, updated on 16-Apr-2024

    Summary

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    Official Symbol
    LY75provided by HGNC
    Official Full Name
    lymphocyte antigen 75provided by HGNC
    Primary source
    HGNC:HGNC:6729
    See related
    Ensembl:ENSG00000054219 MIM:604524; AllianceGenome:HGNC:6729
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CD205; LY-75; CLEC13B; DEC-205; GP200-MR6
    Summary
    Predicted to enable signaling receptor activity. Predicted to be involved in immune response and inflammatory response. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in lymph node (RPKM 17.2), appendix (RPKM 13.2) and 17 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LY75 in Genome Data Viewer
    Location:
    2q24.2
    Exon count:
    35
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (159803355..159904756, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (160260710..160363008, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (160659866..160761267, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:160568592-160569258 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12044 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:160594100-160595092 Neighboring gene membrane associated ring-CH-type finger 7 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_53909 Neighboring gene LY75-CD302 readthrough Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_53950 Neighboring gene uncharacterized LOC124906083 Neighboring gene CD302 molecule Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16688 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16689 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12045 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16690 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16691 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16692 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16695 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16694 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16693 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:160761228-160761469 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16696 Neighboring gene phospholipase A2 receptor 1 Neighboring gene uncharacterized LOC105373717 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:160911725-160912406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16697 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:160982362-160982960 Neighboring gene integrin subunit beta 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:161037195-161037767 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:161037768-161038339

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. LY75 Ablation Mediates Mesenchymal-Epithelial Transition (MET) in Epithelial Ovarian Cancer (EOC) Cells Associated with DNA Methylation Alterations and Suppression of the Wnt/β-Catenin Pathway. Mehdi S, et al. Int J Mol Sci, 2020 Mar 7. PMID 32156068, Free PMC Article
    2. Lymphocyte Antigen 75 Polymorphisms Are Associated with Disease Susceptibility and Phenotype in Japanese Patients with Inflammatory Bowel Disease. Hirayama A, et al. Dis Markers, 2016. PMID 27965521, Free PMC Article
    3. Keratin mediates the recognition of apoptotic and necrotic cells through dendritic cell receptor DEC205/CD205. Cao L, et al. Proc Natl Acad Sci U S A, 2016 Nov 22. PMID 27821726, Free PMC Article
    4. The mannose receptor LY75 (DEC205/CD205) modulates cellular phenotype and metastatic potential of ovarian cancer cells. Faddaoui A, et al. Oncotarget, 2016 Mar 22. PMID 26871602, Free PMC Article
    5. pH-Dependent recognition of apoptotic and necrotic cells by the human dendritic cell receptor DEC205. Cao L, et al. Proc Natl Acad Sci U S A, 2015 Jun 9. PMID 26039988, Free PMC Article

    See all (40) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Interaction of human dendritic cell receptor DEC205/CD205 with keratins.
      Title: Interaction of human dendritic cell receptor DEC205/CD205 with keratins.
    2. LY75 Suppression in Mesenchymal Epithelial Ovarian Cancer Cells Generates a Stable Hybrid EOC Cellular Phenotype, Associated with Enhanced Tumor Initiation, Spreading and Resistance to Treatment in Orthotopic Xenograft Mouse Model.
      Title: LY75 Suppression in Mesenchymal Epithelial Ovarian Cancer Cells Generates a Stable Hybrid EOC Cellular Phenotype, Associated with Enhanced Tumor Initiation, Spreading and Resistance to Treatment in Orthotopic Xenograft Mouse Model.
    3. LY75 Ablation Mediates Mesenchymal-Epithelial Transition (MET) in Epithelial Ovarian Cancer (EOC) Cells Associated with DNA Methylation Alterations and Suppression of the Wnt/beta-Catenin Pathway.
      Title: LY75 Ablation Mediates Mesenchymal-Epithelial Transition (MET) in Epithelial Ovarian Cancer (EOC) Cells Associated with DNA Methylation Alterations and Suppression of the Wnt/β-Catenin Pathway.
    4. combined panel had the highest sensitivity and specificity at 96.3% and 100%, which was significantly or marginally higher than those of EZH2, C-KIT, and CD205 alone
      Title: An immunohistochemical panel consisting of EZH2, C-KIT, and CD205 is useful for distinguishing thymic squamous cell carcinoma from type B3 thymoma.
    5. keratins are the cellular ligands of human DEC205.
      Title: Keratin mediates the recognition of apoptotic and necrotic cells through dendritic cell receptor DEC205/CD205.
    6. High LY75 expression is associated with metastasis of ovarian cancer.
      Title: The mannose receptor LY75 (DEC205/CD205) modulates cellular phenotype and metastatic potential of ovarian cancer cells.
    7. IL-6, DEC205, and CD86 can be predictive biomarkers for the respiratory and immune effects of ambient PM2.5.
      Title: Effects of Components of PM(2.5) Collected in Japan on the Respiratory and Immune Systems.
    8. LY75 Gene Polymorphisms are Associated with Inflammatory Bowel Disease.
      Title: Lymphocyte Antigen 75 Polymorphisms Are Associated with Disease Susceptibility and Phenotype in Japanese Patients with Inflammatory Bowel Disease.
    9. results suggest that DEC205 is an immune receptor that recognizes apoptotic and necrotic cells specifically through a pH-dependent mechanism
      Title: pH-Dependent recognition of apoptotic and necrotic cells by the human dendritic cell receptor DEC205.
    10. Variants in LY75 were associated with a Crohn's disease phenotype involving erythema nodosum.
      Title: Identification of risk loci for Crohn's disease phenotypes using a genome-wide association study.
    Submit: New GeneRIF Correction See all GeneRIFs (24)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Risk HLA-DQA1 and PLA(2)R1 alleles in idiopathic membranous nephropathy.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of LY75 PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 interacts with LY75; predicted interaction to be relevant to viral egress at plasma membrane/extracellular matrix PubMed
    Tat tat Microarray analysis indicates HIV-1 Tat-induced upregulation of lymphocyte antigen 75 (LY75) in primary human brain microvascular endothelial cells PubMed
    capsid gag When introduced the HIV p24 gag protein into a mAb that targets DEC-205/CD205, an endocytic receptor of DCs, low doses of alphaDEC-gag, but not control Ig-gag, stimulates proliferation and IFN-gamma production by CD8+ T cells from HIV-infected donors PubMed

    Go to the HIV-1, Human Interaction Database

    General gene information

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    Markers

    Readthrough LY75-CD302

    Readthrough gene: LY75-CD302, Included gene: CD302

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables carbohydrate binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables signaling receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in endocytosis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in immune response TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in inflammatory response TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in external side of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    lymphocyte antigen 75
    Names
    C-type lectin domain family 13 member B

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_002349.4 → NP_002340.2  lymphocyte antigen 75 precursor

      See identical proteins and their annotated locations for NP_002340.2

      Status: VALIDATED

      Source sequence(s)
      AA279177, AB208915, AF011333, AU099700, DB135177, DB146492, DB150194
      Consensus CDS
      CCDS2211.1
      UniProtKB/Swiss-Prot
      O60449, O75913, Q53R46, Q53TF5, Q7Z575, Q7Z577
      Related
      ENSP00000263636.4, ENST00000263636.5
      Conserved Domains (4) summary
      smart00059
      Location:162 → 209
      FN2; Fibronectin type 2 domain
      cd00037
      Location:1115 → 1222
      CLECT; C-type lectin (CTL)/C-type lectin-like (CTLD) domain
      smart00034
      Location:361 → 486
      CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
      smart00458
      Location:38 → 112
      RICIN; Ricin-type beta-trefoil

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      159803355..159904756 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      160260710..160363008 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O60449.3 GenPept UniProtKB/Swiss-Prot:O60449

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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